Amphi-Panamic Geminates of Snook (Percoidei: Centropomidae) Provide a Calibration of the Divergence Rate in the Mitochondrial DNA Control Region of Fishes

Contrasts in genetic structure and historical demography of marine and riverine populations of Atherina at similar geographical scales

“…These estimates are, however, necessary to compute estimates of effective population size and their changes with time from molecular data. In the absence of a specific calibration for the control region of atherinids, we assumed two very distinct rates: 3.6% and 18.6% divergence per million years, as these rates have been reported for the mtDNA control region in telelosts (Donaldson and Wilson (1999) and Domingues et al (2005), respectively). Despite showing a bimodal distribution (not shown), the pairwise mismatch distributions of Atherina presbyter were not significantly different from the sudden expansion model for the whole studied area (SSD ¼ 0.005, P ¼ 0.827).…”

Phylogeny of the shanny, Lipophrys pholis, from the NE Atlantic using mitochondrial DNA markers

“…Taking into account that early Pleistocene is a plausible period for this separation to occur, the mutation rate aVecting the CR of L. pholis would range between 2.9 and 5.5%, values also encountered in other Wsh species with similar transtion/transversion rate (McMillian and Palumbi, 1997). A reliable calibration of the CR clock for teleosts is provided by the comparison between two amphi-Panamic geminate species of snook (Donaldson and Wilson, 1999), and using this estimate, separation between continental and Azorean shannies occurred about 1 Mya.…”

Genetic characterisation of populations of the critically endangered Goliath grouper ( Epinephelus itajara, Serranidae) from the Northern Brazilian coast through analyses of mtDNA

“…A variety of tests were used to detect possible processes of demographic fluctuation: pairwise mismatch distribution of the haplotypes (Rogers and Harpending, 1992); the sum of the squared deviations (SSD) and its respective p value, which represents the probability of observing a match between the model of expansion and the random distribution; estimate of the expansion time of the population (t), following the Rogers and Harpending (1992) model; and the parameters τ (unit of population growth), θ 0 and θ 1 (θ values before and after expansion, respectively) based on the mismatch distribution, according to the equation t = τ/2u, where u is the mutation rate per sequence per generation (Rogers, 1995;Schneider and Excoffier, 1999). The D-loop mutation rate adopted here was 3.6 × 10 -8 (Donaldson and Wilson, 1999), which was the same one used for other epinephilids (Rivera et al, 2004) and generation time for E. itajara was considered to be six and a half years (Bullock et al, 1992). Effective population size (Ne) was inferred given the estimate of diversity index (θ = 2Neμ) based on Watterson (1975) and Tajima (1983) estimates of θ (θ S and θ π , respectively) in Arlequin 3.1.…”